Mutation in Y STRs: Repeat motif gains vs. losses

Abstract

Y chromosome specific short tandem repeats (Y-STRs) are widely used in population genetics and forensics. Since these markers do not recombine, mutation is the only source of diversity. The primary mutational mechanism leading to length changes in STRs is thought to be polymerase template slippage, and the most common change is the gain or the loss of one repeat motif. In this work, we aim to study 19 Y-STR alleles’ contraction and expansion. Alleles were grouped into tertiles: short (1st tertile), intermediate (2nd tertile) and long alleles (3rd tertile). Significant differences between repeat gains and losses were found at four markers - DYS19, DYS439 for intermediate alleles, and DYS570 and DYS626 for long alleles. When the average number is computed for the pooled loci, for short alleles, the number of repeat motif gains is higher than of repeat losses, and the opposite happens for long alleles. For intermediate alleles, the proportion between the number of repeat gains and losses is close to one. Generally, the rate of expansion decreases from the first tertile to the third, and conversely, the rate of contraction increases from the first tertile to the third. The pooled loci tertiles’ mutation rate increases from short to long alleles. Our results demonstrate that the mutation direction and rate depend on alleles’ length. The longer the allele the greater the mutation and contraction rates.